Getting help | Introduction | Methods | Simulation | Operation | Quantification and data import | DTU testing | Workflow | Salmon quantification | Importing counts into R/Bioconductor | Transcript-to-gene mapping | Statistical analysis of differential transcript usage | DRIMSeq | stageR following DRIMSeq | Post-hoc filtering on the standard deviation in proportions | DEXSeq | stageR following DEXSeq | Citing methods in published research | DTU analysis complements DGE analysis | DGE analysis with DESeq2 | DGE analysis with edgeR | End of workflow section | Discussion | Session information | Software versions | Data availability | Acknowledgments | References
Package: rnaseqDTU 1.33.0
Michael Love
rnaseqDTU: RNA-seq workflow for differential transcript usage following Salmon quantification
RNA-seq workflow for differential transcript usage (DTU) following Salmon quantification. This workflow uses Bioconductor packages tximport, DRIMSeq, and DEXSeq to perform a DTU analysis on simulated data. It also shows how to use stageR to perform two-stage testing of DTU, a statistical framework to screen at the gene level and then confirm which transcripts within the significant genes show evidence of DTU.
Authors:
rnaseqDTU_1.33.0.tar.gz
rnaseqDTU_1.33.0.zip(r-4.7-any)rnaseqDTU_1.33.0.zip(r-4.6-any)rnaseqDTU_1.33.0.zip(r-4.5-any)
rnaseqDTU_1.33.0.tgz(r-4.6-any)rnaseqDTU_1.33.0.tgz(r-4.5-any)
rnaseqDTU_1.33.0.tar.gz(r-4.7-any)rnaseqDTU_1.33.0.tar.gz(r-4.6-any)
rnaseqDTU_1.33.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
rnaseqDTU/json (API)
| # Install 'rnaseqDTU' in R: |
| install.packages('rnaseqDTU', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/thelovelab/rnaseqdtu/issues
Datasets:
- cts - Estimated Salmon counts
- dge.genes - Genes with differential gene expression
- disps - Transcript-level dispersion parameter
- dte.genes - Genes with differential transcript expression
- dtu.genes - Genes with differential transcript usage
- dxr - DEXSeq transcript-level results
- dxr.g - DEXSeq gene-level results
- fold_changes - Simulation fold changes
- frag_GC_bias - Fragment GC bias
- iso.dge - Isoforms in the genes with DGE
- iso.dte - Isoforms with DTE
- iso.dte.only - Isoforms with DTE and not DTU
- iso.dtu - Isoforms with DTU
- res - DRIMSeq gene-level results
- res.txp - DRIMSeq transcript-level results
- sim_counts - Simulated counts for group 1
- sim.counts.mat - Simulated counts
- tpms - Simulated abundances
- txdf - Transcript-to-gene data.frame
- txi.g - Gene-level tximport object
On BioConductor:rnaseqDTU-1.33.0(workflows 3.24)rnaseqDTU-1.32.0(workflows 3.23)
workflowgeneexpressionworkflowimmunooncologyworkflow
Last updated from:1c1db86125. Checks:8 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 175 | ||
| linux-devel | WARNING | 348 | ||
| source / vignettes | OK | 365 | ||
| linux-release | WARNING | 322 | ||
| macos-release | WARNING | 205 | ||
| macos-oldrel | WARNING | 163 | ||
| windows-devel | WARNING | 151 | ||
| windows-release | WARNING | 172 | ||
| windows-oldrel | WARNING | 202 | ||
| wasm-release | OK | 172 |
Exports:
Dependencies:abindannotateAnnotationDbiaskpassbase64encBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocManagerBiocParallelbiomaRtBiostringsbitbit64bitopsblobbrewbriobslibcachemcallrclicliprcodetoolscommonmarkcpp11crayoncredentialscurlDBIdbplyrDelayedArraydescDESeq2devtoolsDEXSeqdiffobjdigestdownlitdplyrDRIMSeqedgeRellipsisevaluatefansifarverfastmapfilelockfontawesomeformatRfsfutile.loggerfutile.optionsgenefiltergeneplottergenericsGenomicRangesgertggplot2gitcredsgluegtablehighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2hwriteriniIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimeminiUIopensslotelpakpillarpkgbuildpkgconfigpkgdownpkgloadplyrpngpraiseprettyunitsprocessxprofvisprogresspromisespspurrrR6rafalibraggrappdirsrcmdcheckRColorBrewerRcppRcppArmadillordtoolsreshape2Rhtslibrlangrmarkdownroxygen2rprojrootRsamtoolsRSQLiterstudioapirversionsS4ArraysS4VectorsS7sassscalesSeqinfosessioninfoshinysnowsourcetoolsSparseArraystageRstatmodstringistringrSummarizedExperimentsurvivalsyssystemfontstestthattextshapingtibbletidyrtidyselecttinytexurlcheckerusethisutf8vctrsviridisLitewaldowhiskerwithrxfunXMLxml2xopenxtableXVectoryamlzip
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Estimated Salmon counts (6 vs 6) | cts |
| Genes with differential gene expression | dge.genes |
| Transcript-level dispersion parameter | disps |
| Genes with differential transcript expression | dte.genes |
| Genes with differential transcript usage | dtu.genes |
| DEXSeq transcript-level results | dxr |
| DEXSeq gene-level results | dxr.g |
| Simulation fold changes | fold_changes |
| Fragment GC bias | frag_GC_bias |
| Isoforms in the genes with DGE | iso.dge |
| Isoforms with DTE | iso.dte |
| Isoforms with DTE and not DTU | iso.dte.only |
| Isoforms with DTU | iso.dtu |
| DRIMSeq gene-level results | res |
| DRIMSeq transcript-level results | res.txp |
| Simulated counts for group 1 | sim_counts |
| Simulated counts | sim.counts.mat |
| Simulated abundances | tpms |
| Transcript-to-gene data.frame | txdf |
| Gene-level tximport object | txi.g |